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Class: EntityToDiseaseAssociationMixin

Description: mixin class for any association whose object (target node) is a disease
classDiagram class EntityToDiseaseAssociationMixin EntityToFeatureOrDiseaseQualifiersMixin <|-- EntityToDiseaseAssociationMixin EntityToDiseaseAssociationMixin <|-- CorrelatedGeneToDiseaseAssociation EntityToDiseaseAssociationMixin <|-- DruggableGeneToDiseaseAssociation EntityToDiseaseAssociationMixin <|-- PhenotypicFeatureToDiseaseAssociation EntityToDiseaseAssociationMixin <|-- VariantToDiseaseAssociation EntityToDiseaseAssociationMixin <|-- GenotypeToDiseaseAssociation EntityToDiseaseAssociationMixin <|-- GeneAsAModelOfDiseaseAssociation EntityToDiseaseAssociationMixin <|-- VariantAsAModelOfDiseaseAssociation EntityToDiseaseAssociationMixin <|-- GenotypeAsAModelOfDiseaseAssociation EntityToDiseaseAssociationMixin <|-- CellLineAsAModelOfDiseaseAssociation EntityToDiseaseAssociationMixin <|-- OrganismalEntityAsAModelOfDiseaseAssociation EntityToDiseaseAssociationMixin : disease_context_qualifier EntityToDiseaseAssociationMixin --|> Disease : disease_context_qualifier EntityToDiseaseAssociationMixin : frequency_qualifier EntityToDiseaseAssociationMixin : object EntityToDiseaseAssociationMixin --|> Disease : object EntityToDiseaseAssociationMixin : object_aspect_qualifier EntityToDiseaseAssociationMixin --|> GeneOrGeneProductOrChemicalEntityAspectEnum : object_aspect_qualifier EntityToDiseaseAssociationMixin : object_direction_qualifier EntityToDiseaseAssociationMixin --|> DirectionQualifierEnum : object_direction_qualifier EntityToDiseaseAssociationMixin : predicate EntityToDiseaseAssociationMixin : qualified_predicate EntityToDiseaseAssociationMixin : subject EntityToDiseaseAssociationMixin --|> NamedThing : subject EntityToDiseaseAssociationMixin : subject_aspect_qualifier EntityToDiseaseAssociationMixin --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier EntityToDiseaseAssociationMixin : subject_direction_qualifier EntityToDiseaseAssociationMixin --|> DirectionQualifierEnum : subject_direction_qualifier

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
subject_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).
0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 EntityToFeatureOrDiseaseQualifiersMixin stability, abundance, expression, exposure
subject_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). 		0..1
DirectionQualifierEnum		 EntityToFeatureOrDiseaseQualifiersMixin increased, downregulated
object_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement). 		0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 EntityToFeatureOrDiseaseQualifiersMixin stability, abundance, expression, exposure
object_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). 		0..1
DirectionQualifierEnum		 EntityToFeatureOrDiseaseQualifiersMixin increased, downregulated
qualified_predicate:
Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. 		0..1
Uriorcurie		 EntityToFeatureOrDiseaseQualifiersMixin biolink:causes
disease_context_qualifier:
A context qualifier representing a disease or condition in which a relationship expressed in an association took place. 		0..1
Disease		 EntityToFeatureOrDiseaseQualifiersMixin MONDO:0004979, MONDO:0005148
frequency_qualifier:
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject 		0..1
FrequencyValue		 FrequencyQualifierMixin
subject:
connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. 		1
NamedThing		 FrequencyQualifierMixin
predicate:
Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats 		1
Uriorcurie		 FrequencyQualifierMixin
object:
disease 		1
Disease		 FrequencyQualifierMixin MONDO:0020066

Mixin Usage

mixed into description
CorrelatedGeneToDiseaseAssociation An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score.
DruggableGeneToDiseaseAssociation An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers).
PhenotypicFeatureToDiseaseAssociation An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease.
VariantToDiseaseAssociation An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state.
GenotypeToDiseaseAssociation An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state.
GeneAsAModelOfDiseaseAssociation An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease.
VariantAsAModelOfDiseaseAssociation An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.
GenotypeAsAModelOfDiseaseAssociation An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.
CellLineAsAModelOfDiseaseAssociation An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings.
OrganismalEntityAsAModelOfDiseaseAssociation An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it.

LinkML Source

name: entity to disease association mixin
description: mixin class for any association whose object (target node) is a disease
from_schema: https://w3id.org/biolink/vocab/
is_a: entity to feature or disease qualifiers mixin
mixin: true
slot_usage:
  object:
    name: object
    description: disease
    examples:
    - value: MONDO:0020066
      description: Ehlers-Danlos syndrome
    range: disease
defining_slots:
- object